The exit status of the task that caused the workflow execution to fail was: 102.
The full error message was:
Error executing process > 'STAR_Fusion (268)' Caused by: Process `STAR_Fusion (268)` terminated with an error exit status (102) Command executed: set -eou pipefail STAR --genomeDir $PWD/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --runThreadN 8 --readFilesIn SJCBF022_D.RNA-Seq_r1.fastq.gz SJCBF022_D.RNA-Seq_r2.fastq.gz --outFileNamePrefix SJCBF022_D.RNA-Seq_ --outReadsUnmapped None --twopassMode Basic --twopass1readsN -1 --readFilesCommand "gunzip -c" --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 63004036730 --outSAMattributes NH HI NM MD AS nM jM jI XS --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimFilter banGenomicN /usr/local/src/STAR-Fusion/STAR-Fusion --genome_lib_dir $PWD/ctat_genome_lib_build_dir --chimeric_junction "SJCBF022_D.RNA-Seq_Chimeric.out.junction" --left_fq SJCBF022_D.RNA-Seq_r1.fastq.gz --right_fq SJCBF022_D.RNA-Seq_r2.fastq.gz --CPU 8 --FusionInspector inspect --examine_coding_effect --denovo_reconstruct --output_dir SJCBF022_D.RNA-Seq_ echo ---------------------------------------- echo "list all output files in /home/jlsmith3/scripts/STAR-fusion-NF" ls -1 $PWD echo ----------------------------------------- echo "list all output files in sample directory" ls -1 SJCBF022_D.RNA-Seq_ Command exit status: 102 Command output: Sep 28 02:27:19 ..... started STAR run Sep 28 02:27:19 ..... loading genome Sep 28 02:27:37 ..... started 1st pass mapping Sep 28 02:57:11 ..... finished 1st pass mapping Sep 28 02:57:12 ..... inserting junctions into the genome indices Sep 28 03:01:02 ..... started mapping Sep 28 03:44:19 ..... finished mapping Sep 28 03:44:22 ..... started sorting BAM Command error: EXITING because of fatal ERROR: not enough memory for BAM sorting: SOLUTION: re-run STAR with at least --limitBAMsortRAM 64523905173 Sep 28 03:44:22 ...... FATAL ERROR, exiting Work dir: s3://fh-pi-meshinchi-s/SR/work/95/fc9128ddca0410904344919934facf Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
nextflow run -c /home/jlsmith3/nextflow.config STAR_Fusion.nf --sample_sheet sample_sheets/st.jude_sample_sheet.txt --genome_lib 's3://fh-pi-meshinchi-s/SR/Reference_Data/GRCh37_gencode_v19_CTAT_lib_Oct012019/ctat_genome_lib_build_dir/' --output_folder 's3://fh-pi-meshinchi-s/SR/starfusion/' -with-report STAR-Fusion_St.Jude_report.html -work-dir 's3://fh-pi-meshinchi-s/SR/work' -cache TRUE -process.queue cpu-spot-50 ' #temporary' bc spot-30 is not really working50215d3e1bcdea339a046d7127b8243ee25f3dfe-aca8-4a04-aea4-72928f6a284fThese plots give an overview of the distribution of resource usage for each process.
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